{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T11:25:59Z","timestamp":1791804359535,"version":"4.3.4"},"reference-count":111,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2023,6,23]],"date-time":"2023-06-23T00:00:00Z","timestamp":1687478400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Union's Horizon 2020","award":["824110"],"award-info":[{"award-number":["824110"]}]},{"name":"Instand-NGS4P","award":["874719"],"award-info":[{"award-number":["874719"]}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["407495230"],"award-info":[{"award-number":["407495230"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["314905040"],"award-info":[{"award-number":["314905040"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["497786653"],"award-info":[{"award-number":["497786653"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["493697503"],"award-info":[{"award-number":["493697503"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Competence Center for Genomic Analysis (CCGA) Kiel","award":["423957469"],"award-info":[{"award-number":["423957469"]}]},{"DOI":"10.13039\/501100005972","name":"German Cancer Aid","doi-asserted-by":"publisher","award":["70113922"],"award-info":[{"award-number":["70113922"]}],"id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Instituto de Salud Carlos III","award":["PI19\/01772"],"award-info":[{"award-number":["PI19\/01772"]}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["MINECO\/FEDER"],"award-info":[{"award-number":["MINECO\/FEDER"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["BIO2015-71792-P"],"award-info":[{"award-number":["BIO2015-71792-P"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,8,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation\u00a0and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp\/Q41 bp\u00a0=\u00a05%). Finally, we provide a checklist called \u2018ERROR-FFPE-DNA\u2019\u00a0that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.<\/jats:p>","DOI":"10.1093\/nar\/gkad519","type":"journal-article","created":{"date-parts":[[2023,6,8]],"date-time":"2023-06-08T04:11:46Z","timestamp":1686197506000},"page":"7143-7162","source":"Crossref","is-referenced-by-count":95,"title":["A critical spotlight on the paradigms of FFPE-DNA sequencing"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0125-1173","authenticated-orcid":false,"given":"Tim A","family":"Steiert","sequence":"first","affiliation":[{"name":"Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein , Kiel\u00a024105 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gen\u00eds","family":"Parra","sequence":"additional","affiliation":[{"name":"Center for Genomic Regulation, Centro Nacional de An\u00e1lisis Gen\u00f3mico , Barcelona\u00a008028 , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Gut","sequence":"additional","affiliation":[{"name":"Center for Genomic Regulation, Centro Nacional de An\u00e1lisis Gen\u00f3mico , Barcelona\u00a008028 , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norbert","family":"Arnold","sequence":"additional","affiliation":[{"name":"Department of Gynaecology and Obstetrics, University Medical Center Schleswig-Holstein , Campus Kiel , Kiel\u00a024105 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-R\u00e9mi","family":"Trotta","sequence":"additional","affiliation":[{"name":"Center for Genomic Regulation, Centro Nacional de An\u00e1lisis Gen\u00f3mico , Barcelona\u00a008028 , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ra\u00fal","family":"Tonda","sequence":"additional","affiliation":[{"name":"Center for Genomic Regulation, Centro Nacional de An\u00e1lisis Gen\u00f3mico , Barcelona\u00a008028 , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice","family":"Moussy","sequence":"additional","affiliation":[{"name":"Le Centre de r\u00e9f\u00e9rence, d\u2019innovation, d\u2019expertise et de transfert (CRefIX), PFMG 2025 , \u00c9vry\u00a091057 , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuzana","family":"Gerber","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine (CNRGH), Institut de Biologie Fran\u00e7ois Jacob, CEA, Universit\u00e9 Paris-Saclay , \u00c9vry\u00a091057 , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter\u00a0M","family":"Abuja","sequence":"additional","affiliation":[{"name":"Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz , Graz\u00a08010 , Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kurt","family":"Zatloukal","sequence":"additional","affiliation":[{"name":"Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz , Graz\u00a08010 , Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6989-8002","authenticated-orcid":false,"given":"Christoph","family":"R\u00f6cken","sequence":"additional","affiliation":[{"name":"Department of Pathology, University Medical Center Schleswig-Holstein , Campus Kiel , Kiel\u00a024105 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trine","family":"Folseraas","sequence":"additional","affiliation":[{"name":"Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet , Oslo\u00a00372 , Norway"},{"name":"Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet , Oslo\u00a00372 , Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marit\u00a0M","family":"Grimsrud","sequence":"additional","affiliation":[{"name":"Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet , Oslo\u00a00372 , Norway"},{"name":"Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , Oslo\u00a00372 , Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arndt","family":"Vogel","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School , Hanover\u00a030625 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Goeppert","sequence":"additional","affiliation":[{"name":"Institute of Pathology, University Hospital Heidelberg , Heidelberg\u00a069120 , Germany"},{"name":"Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg , Ludwigsburg\u00a071640 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5333-5942","authenticated-orcid":false,"given":"Stephanie","family":"Roessler","sequence":"additional","affiliation":[{"name":"Institute of Pathology, University Hospital Heidelberg , Heidelberg\u00a069120 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Hinz","sequence":"additional","affiliation":[{"name":"Department of General Surgery, University Medicine Rostock , Rostock\u00a018057 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clemens","family":"Schafmayer","sequence":"additional","affiliation":[{"name":"Department of General Surgery, University Medicine Rostock , Rostock\u00a018057 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Rosenstiel","sequence":"additional","affiliation":[{"name":"Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein , Kiel\u00a024105 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5358-4463","authenticated-orcid":false,"given":"Jean-Fran\u00e7ois","family":"Deleuze","sequence":"additional","affiliation":[{"name":"Le Centre de r\u00e9f\u00e9rence, d\u2019innovation, d\u2019expertise et de transfert (CRefIX), PFMG 2025 , \u00c9vry\u00a091057 , France"},{"name":"Centre National de Recherche en G\u00e9nomique Humaine (CNRGH), Institut de Biologie Fran\u00e7ois Jacob, CEA, Universit\u00e9 Paris-Saclay , \u00c9vry\u00a091057 , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7219-632X","authenticated-orcid":false,"given":"Ivo\u00a0G","family":"Gut","sequence":"additional","affiliation":[{"name":"Center for Genomic Regulation, Centro Nacional de An\u00e1lisis Gen\u00f3mico , Barcelona\u00a008028 , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andre","family":"Franke","sequence":"additional","affiliation":[{"name":"Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein , Kiel\u00a024105 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9927-5124","authenticated-orcid":false,"given":"Michael","family":"Forster","sequence":"additional","affiliation":[{"name":"Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein , Kiel\u00a024105 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,6,23]]},"reference":[{"key":"2023081100511482800_B1","first-page":"229","article-title":"Notiz \u00fcber die Anwendung des Formaldehyds (Formol) als H\u00e4rtungs-und Konservierungsmittel","volume":"9","author":"Blum","year":"1894","journal-title":"Anat. Anz."},{"key":"2023081100511482800_B2","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/s12907-016-0039-3","article-title":"Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality","volume":"16","author":"Seiler","year":"2016","journal-title":"BMC Clin. Pathol."},{"key":"2023081100511482800_B3","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1002\/1096-9896(200109)195:1<66::AID-PATH921>3.0.CO;2-F","article-title":"Unlocking the archive\u2013gene expression in paraffin-embedded tissue","volume":"195","author":"Lewis","year":"2001","journal-title":"J. Pathol."},{"key":"2023081100511482800_B4","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.3390\/ijms17091579","article-title":"Pre-analytical considerations for successful next-generation sequencing (NGS): challenges and opportunities for formalin-fixed and paraffin-embedded tumor tissue (FFPE) samples","volume":"17","author":"Arreaza","year":"2016","journal-title":"Int. J. Mol. Sci."},{"key":"2023081100511482800_B5","doi-asserted-by":"crossref","first-page":"1941","DOI":"10.1002\/ijc.31937","article-title":"Estimating the global cancer incidence and mortality in 2018: GLOBOCAN sources and methods","volume":"144","author":"Ferlay","year":"2019","journal-title":"Int. J. Cancer"},{"key":"2023081100511482800_B6","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1093\/bfgp\/elm023","article-title":"Biobanks: transnational, European and global networks","volume":"6","author":"Asslaber","year":"2007","journal-title":"Brief. Funct. Genomics Proteomics"},{"key":"2023081100511482800_B7","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1186\/s13059-022-02709-8","article-title":"Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples","volume":"23","author":"Zhang","year":"2022","journal-title":"Genome Biol."},{"key":"2023081100511482800_B8","doi-asserted-by":"crossref","first-page":"4487","DOI":"10.1038\/s41467-022-32041-5","article-title":"The mutational signatures of formalin fixation on the human genome","volume":"13","author":"Guo","year":"2022","journal-title":"Nat. Commun."},{"key":"2023081100511482800_B9","doi-asserted-by":"crossref","first-page":"jkac238","DOI":"10.1093\/g3journal\/jkac238","article-title":"Analyses of mutational patterns induced by formaldehyde and acetaldehyde reveal similarity to a common mutational signature","volume":"12","author":"Thapa","year":"2022","journal-title":"G3 - Genes Genomes Genet."},{"key":"2023081100511482800_B10","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1038\/s41587-021-00994-5","article-title":"Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing","volume":"39","author":"Xiao","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"2023081100511482800_B11","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1016\/S0002-9440(10)64472-0","article-title":"Effect of fixatives and tissue processing on the content and integrity of nucleic acids","volume":"161","author":"Srinivasan","year":"2002","journal-title":"Am. J. Pathol."},{"key":"2023081100511482800_B12","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/0378-4347(84)80202-9","article-title":"Rapid isolation, hydrolysis and chromatography of formaldehyde-modified DNA","volume":"308","author":"Beland","year":"1984","journal-title":"J. Chromatogr. B Biomed. Appl."},{"key":"2023081100511482800_B13","doi-asserted-by":"crossref","first-page":"3267","DOI":"10.1021\/bi00634a001","article-title":"Formaldehyde as a probe of DNA structure. 3. Equilibrium denaturation of DNA and synthetic polynucleotides","volume":"16","author":"McGhee","year":"1977","journal-title":"Biochemistry"},{"key":"2023081100511482800_B14","doi-asserted-by":"crossref","first-page":"e537","DOI":"10.1371\/journal.pone.0000537","article-title":"The isolation of nucleic acids from fixed, paraffin-embedded tissues\u2013which methods are useful when?","volume":"2","author":"Gilbert","year":"2007","journal-title":"PLoS One"},{"key":"2023081100511482800_B15","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/S0027-5107(97)00314-X","article-title":"DNA damage caused by common cytological fixatives","volume":"401","author":"Douglas","year":"1998","journal-title":"Mutat. Res. - Fundam. Mol. Mech."},{"key":"2023081100511482800_B16","doi-asserted-by":"crossref","first-page":"3618","DOI":"10.1021\/bi00769a019","article-title":"Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid","volume":"11","author":"Lindahl","year":"1972","journal-title":"Biochemistry"},{"key":"2023081100511482800_B17","doi-asserted-by":"crossref","first-page":"e115950","DOI":"10.1371\/journal.pone.0115950","article-title":"Non-enzymatic depurination of nucleic acids: factors and mechanisms","volume":"9","author":"An","year":"2014","journal-title":"PLoS One"},{"key":"2023081100511482800_B18","doi-asserted-by":"crossref","first-page":"4518","DOI":"10.1021\/bi00288a026","article-title":"Insertion of nucleotides opposite apurinic apyrimidinic sites in deoxyribonucleic acid during in vitro synthesis: uniqueness of adenine nucleotides","volume":"22","author":"Sagher","year":"1983","journal-title":"Biochemistry"},{"key":"2023081100511482800_B19","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.bbrc.2007.01.169","article-title":"DNA damage reduces Taq DNA polymerase fidelity and PCR amplification efficiency","volume":"355","author":"Sikorsky","year":"2007","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2023081100511482800_B20","doi-asserted-by":"crossref","first-page":"e38881","DOI":"10.1371\/journal.pone.0038881","article-title":"DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues","volume":"7","author":"Craig","year":"2012","journal-title":"PLoS One"},{"key":"2023081100511482800_B21","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1136\/mp.56.3.184","article-title":"PCR analysis in archival postmortem tissues","volume":"56","author":"Bonin","year":"2003","journal-title":"Mol. Pathol."},{"key":"2023081100511482800_B22","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1007\/s40291-014-0115-2","article-title":"Cytosine deamination is a major cause of baseline noise in next-generation sequencing","volume":"18","author":"Chen","year":"2014","journal-title":"Mol. Diagn. Ther."},{"key":"2023081100511482800_B23","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1373\/clinchem.2012.202390","article-title":"Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates","volume":"59","author":"Do","year":"2013","journal-title":"Clin. Chem."},{"key":"2023081100511482800_B24","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/1476-4598-8-82","article-title":"Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies","volume":"8","author":"Do","year":"2009","journal-title":"Mol. 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Cytochem."},{"key":"2023081100511482800_B30","doi-asserted-by":"crossref","first-page":"79","DOI":"10.2144\/btn-2018-0016","article-title":"Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests","volume":"65","author":"Mill\u00e1n-Esteban","year":"2018","journal-title":"Biotechniques"},{"key":"2023081100511482800_B31","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1007\/s13402-014-0196-2","article-title":"Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology","volume":"37","author":"Sie","year":"2014","journal-title":"Cell. Oncol."},{"key":"2023081100511482800_B32","doi-asserted-by":"crossref","first-page":"8908","DOI":"10.1038\/s41598-019-45210-2","article-title":"High-resolution copy number patterns from clinically relevant FFPE material","volume":"9","author":"Filia","year":"2019","journal-title":"Sci. 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Genom."},{"key":"2023081100511482800_B36","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1038\/gim.2017.241","article-title":"Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project","volume":"20","author":"Robbe","year":"2018","journal-title":"Genet. 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Standard."},{"key":"2023081100511482800_B50","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.cca.2018.11.002","article-title":"Relationship between formalin reagent and success rate of targeted sequencing analysis using formalin fixed paraffin embedded tissues","volume":"488","author":"Amemiya","year":"2019","journal-title":"Clin. Chim. Acta"},{"key":"2023081100511482800_B51","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.jss.2017.06.077","article-title":"Formalin-fixed paraffin-embedded sample conditions for deep next generation sequencing","volume":"220","author":"Nagahashi","year":"2017","journal-title":"J. Surg. Res."},{"key":"2023081100511482800_B52","doi-asserted-by":"crossref","first-page":"2683","DOI":"10.3892\/etm.2017.4797","article-title":"Estimation of age-related DNA degradation from formalin-fixed and paraffin-embedded tissue according to the extraction methods","volume":"14","author":"Watanabe","year":"2017","journal-title":"Exp. 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Chem."},{"key":"2023081100511482800_B63","doi-asserted-by":"crossref","first-page":"8901","DOI":"10.1073\/pnas.90.19.8901","article-title":"Repair of 8-hydroxyguanine in DNA by mammalian N-methylpurine-DNA glycosylase","volume":"90","author":"Bessho","year":"1993","journal-title":"Proc. Natl. Acad. Sci. 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